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Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD‐tag based GBS—insights into species origin and effects of software pipelines
Author(s) -
Qi ZheChen,
Yu Yi,
Liu Xiang,
Pais Andrew,
Ranney Thomas,
Whetten Ross,
Xiang QiuYun Jenny
Publication year - 2015
Publication title -
journal of systematics and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.249
H-Index - 46
eISSN - 1759-6831
pISSN - 1674-4918
DOI - 10.1111/jse.12176
Subject(s) - biology , polyploid , phylogenomics , lineage (genetic) , evolutionary biology , allopatric speciation , phylogenetic tree , ploidy , molecular clock , sanger sequencing , dna sequencing , genetics , population , clade , gene , demography , sociology
Fothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4 x ) from the coastal plains of the southeastern USA, F. major (6 x ) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) was applied to generate genome‐wide molecular markers for phylogenetic and genetic structure analyses of 36 accessions of Fothergilla . Sanger sequencing of three plastid and one nuclear regions provided data for comparison with GBS‐based results. Phylogenetic outcomes were compared using data from different sequencing runs and different software workflows. The different data sets showed substantial differences in inferred phylogenies, but all supported a genetically distinct 6 x F. major and two lineages of the diploid populations closely associated with the 4 x F. gardenii . We hypothesize that the 4 x F. gardenii originated through hybridization between the Gulf coastal 2 x and an extinct (or undiscovered) 2 x lineage, followed by backcrosses to the Atlantic coastal 2 x before chromosome doubling, and the 6 x F. major also originated from the “extinct” 2 x lineage. Alternative scenarios are possible but are not as well supported. The origins and divergence of the polyploid species likely occurred during the Pleistocene cycles of glaciation, although fossil evidence indicates the genus might have existed for a much longer time with a wider past distribution. Our study demonstrates the power of combining GBS data with Sanger sequencing in reconstructing the evolutionary network of polyploid lineages.